An Introduction To Metabolism: Urry - Cain - Wasserman - Minorsky - Reece

CAMPBELL BIOLOGY IN FOCUS
URRY • CAIN • WASSERMAN • MINORSKY • REECE
6
An Introduction
to Metabolism
Lecture Presentations by
Kathleen Fitzpatrick and
Nicole Tunbridge,
Simon Fraser University
© 2016 Pearson Education, Inc. SECOND EDITION

The Energy of Life
 The living cell is a miniature chemical factory where

thousands of reactions occur
 The cell extracts energy and applies energy to
perform work
 Some organisms even convert energy to light, as in
bioluminescence
© 2016 Pearson Education, Inc.

Figure 6.1

Concept 6.1: An organism’s metabolism transforms
matter and energy
 Metabolism is the totality of an organism’s
chemical reactions
 Metabolism is an emergent property of life that
arises from interactions between molecules within
the cell

Metabolic Pathways
 A metabolic pathway begins with a specific

molecule and ends with a product
 Each step is catalyzed by a specific enzyme

Figure 6.UN01
Enzyme 1 Enzyme 2 Enzyme 3

A B C D
Reaction 1 Reaction 2 Reaction 3
Starting Product
molecule

 Catabolic pathways release energy by breaking
down complex molecules into simpler compounds
 One example of catabolism is cellular respiration,
the breakdown of glucose and other organic fuels to
carbon dioxide and water

 Anabolic pathways consume energy to build
complex molecules from simpler ones
 The synthesis of proteins from amino acids is an
example of anabolism
 Bioenergetics is the study of how energy flows
through living organisms

Forms of Energy
 Energy is the capacity to cause change

 Energy exists in various forms, some of which can
perform work

 Kinetic energy is energy associated with motion
 Thermal energy is kinetic energy associated with
random movement of atoms or molecules
 Heat is thermal energy in transfer from one object to
another
 Light is another type of energy that can be
harnessed to perform work

 Potential energy is energy that matter possesses
because of its location or structure
 Chemical energy is potential energy available for
release in a chemical reaction
 Energy can be converted from one form to another

Animation: Energy Concepts

Figure 6.2
A diver has more potential Diving converts
energy on the platform. potential energy to
kinetic energy.
Climbing up converts the kinetic A diver has less

energy of muscle movement potential energy in
to potential energy. the water.
The Laws of Energy Transformation
 Thermodynamics is the study of energy

transformations
 In an open system, energy and matter can be
transferred between the system and its
surroundings
 In an isolated system, exchange with the
surroundings cannot occur
 Organisms are open systems

The First Law of Thermodynamics
 According to the first law of thermodynamics, the

energy of the universe is constant
 Energy can be transferred and or transformed, but it
cannot be created or destroyed
 The first law is also called the principle of
conservation of energy

Figure 6.3
Heat
CO2
H2O
Chemical
energy
(a) First law of thermodynamics (b) Second law of thermodynamics

Figure 6.3-1
Chemical
energy
(a) First law of thermodynamics

The Second Law of Thermodynamics
 During every energy transfer or transformation,

some energy is lost as heat
 According to the second law of thermodynamics
 Every energy transfer or transformation increases the
entropy of the universe
 Entropy is a measure of disorder, or randomness

Figure 6.3-2
Heat
CO2
H2O
(b) Second law of thermodynamics

 Living cells unavoidably convert organized forms of
energy to heat
 Spontaneous processes occur without energy
input; they can happen quickly or slowly
 For a process to occur spontaneously, it must
increase the entropy of the universe

Biological Order and Disorder
 Cells create ordered structures from less ordered

materials
 Organisms also replace ordered forms of matter
and energy with less ordered forms
 Energy flows into an ecosystem in the form of light
and exits in the form of heat

Figure 6.4

Figure 6.4-1

Figure 6.4-2

 The evolution of more complex organisms does not
violate the second law of thermodynamics
 Entropy (disorder) may decrease in a system, but
the universe’s total entropy increases
 Organisms are islands of low entropy in an
increasingly random universe

Concept 6.2: The free-energy change of a reaction
tells us whether or not the reaction occurs
spontaneously
 Biologists measure changes in free energy to help
them understand the chemical reactions of life

Free-Energy Change (G), Stability, and Equilibrium
 A living system’s free energy is energy that can do

work when temperature and pressure are uniform,
as in a living cell

 The change in free energy (∆G) during a chemical
reaction is the difference between the free energy of
the final state and the free energy of the initial state
∆G = Gfinal state – Ginitial state
 Only processes with a negative ∆G are
spontaneous
 Spontaneous processes can be harnessed to
perform work

 Free energy is a measure of a system’s instability,
its tendency to change to a more stable state
 During a spontaneous change, free energy
decreases and the stability of a system increases

Figure 6.5
• More free energy (higher G)

• Less stable
• Greater work capacity
In a spontaneous change
• The free energy of the system
decreases (G < 0)
• The system becomes more
stable
• The released free energy can
be harnessed to do work
• Less free energy (lower G)

• More stable
• Less work capacity (a) Gravitational (b) Diffusion (c) Chemical
motion reaction

Figure 6.5-1
• More free energy (higher G)

• Less stable
• Greater work capacity
In a spontaneous change
• The free energy of the system
decreases (G < 0)
• The system becomes more
stable
• The released free energy can
be harnessed to do work
• Less free energy (lower G)

• More stable
• Less work capacity
Figure 6.5-2
(a) Gravitational (b) Diffusion (c) Chemical

motion reaction

 At equilibrium, forward and reverse reactions occur
at the same rate; it is a state of maximum stability
 A process is spontaneous and can perform work only
when it is moving toward equilibrium

Free Energy and Metabolism
 The concept of free energy can be applied to the

chemistry of life’s processes

Exergonic and Endergonic Reactions in Metabolism
 An exergonic reaction proceeds with a net release

of free energy and is spontaneous; ∆G is negative
 The magnitude of ∆G represents the maximum
amount of work the reaction can perform

Figure 6.6
(a) Exergonic reaction: energy released, spontaneous
Reactants
Amount of
energy
released
Free energy
(G < 0)
Energy
Products
Progress of the reaction
(b) Endergonic reaction: energy required,

nonspontaneous
Products
Amount of
energy
Free energy
required
Energy (G > 0)
Reactants

Figure 6.6-1
(a) Exergonic reaction: energy released, spontaneous
Reactants
Amount of
energy
released
Free energy
(G < 0)
Energy
Products

 An endergonic reaction absorbs free energy from
its surroundings and is nonspontaneous; ∆G is
positive
 The magnitude of ∆G is the quantity of energy
required to drive the reaction

Figure 6.6-2
(b) Endergonic reaction: energy required,

nonspontaneous
Products
Amount of
energy
required
Free energy
(G > 0)
Energy
Reactants

Equilibrium and Metabolism
 Hydroelectric systems can serve as analogies for

chemical reactions in living systems
 Reactions in an isolated system eventually reach
equilibrium and can then do no work

Figure 6.7
G < 0 G = 0
(a) An isolated hydroelectric system
(b) An open
hydroelectric G < 0
system
G < 0
G < 0
G < 0
(c) A multistep open hydroelectric system

Figure 6.7-1
G < 0 G = 0
(a) An isolated hydroelectric system

 Cells are not in equilibrium; they are open systems
experiencing a constant flow of materials

Figure 6.7-2
(b) An open
hydroelectric
system
G < 0

 A catabolic pathway in a cell releases free energy in
a series of reactions
 The product of each reaction is the reactant for the
next, preventing the system from reaching
equilibrium

Figure 6.7-3
G < 0
G < 0
G < 0
(c) A multistep open hydroelectric system

Concept 6.3: ATP powers cellular work by coupling
exergonic reactions to endergonic reactions
 A cell does three main kinds of work
 Chemical
 Transport
 Mechanical

 To do work, cells manage energy resources by
energy coupling, the use of an exergonic process
to drive an endergonic one
 Most energy coupling in cells is mediated by ATP

The Structure and Hydrolysis of ATP
 ATP (adenosine triphosphate) is composed of

ribose (a sugar), adenine (a nitrogenous base), and
three phosphate groups
 In addition to its role in energy coupling, ATP is also
used to make RNA

Video: ATP Space-filling Model

Video: ATP Stick Model

Figure 6.8
Adenine
Triphosphate group
(3 phosphate groups) Ribose
(a) The structure of ATP
P P P
Adenosine triphosphate (ATP)
H2O
Pi P P Energy
Inorganic
Adenosine diphosphate (ADP)
phosphate
(b) The hydrolysis of ATP

Figure 6.8-1
Adenine
Triphosphate group
(3 phosphate groups) Ribose
(a) The structure of ATP

 The bonds between the phosphate groups of ATP
can be broken by hydrolysis
 Energy is released from ATP when the terminal
phosphate bond is broken
 This release of energy comes from the chemical
change to a state of lower free energy, not from the
phosphate bonds themselves

Figure 6.8-2
P P P
Adenosine triphosphate (ATP)
H2O
Pi P P Energy
Inorganic
Adenosine diphosphate (ADP)
phosphate
(b) The hydrolysis of ATP

 ATP hydrolysis releases a lot of energy due to the
repulsive force of the three negatively charged
phosphate groups
 The triphosphate tail of ATP is the chemical
equivalent of a compressed spring

How the Hydrolysis of ATP Performs Work
 The three types of cellular work (mechanical,

transport, and chemical) are powered by the
hydrolysis of ATP
 In the cell, the energy from the exergonic reaction of
ATP hydrolysis can be used to drive endergonic
reactions

 ATP drives endergonic reactions by
phosphorylation, transferring a phosphate group to
some other molecule, such as a reactant
 The recipient molecule is now called a
phosphorylated intermediate
 Overall, the coupled reactions are exergonic

Figure 6.9
NH3 NH2
Glu Glu
GGlu = +3.4 kcal/mol
Glutamic acid Ammonia Glutamine

(a) Glutamic acid conversion to glutamine
NH3
P
NH2 ADP P
ATP ADP i
Glu Glu Glu
Glutamic acid Phosphorylated Glutamine

intermediate
(b) Conversion reaction coupled with ATP hydrolysis
NH3 NH2
Glu ATP ADP P i
Glu

GATP = 7.3 kcal/mol
+ GATP = 7.3 kcal/mol
Net G = 3.9 kcal/mol (c) Free-energy change for coupled reaction

Figure 6.9-1
NH3 NH2
Glu Glu
Glutamic acid Ammonia Glutamine

(a) Glutamic acid conversion to glutamine

Figure 6.9-2
P
ATP ADP
Glu Glu
Glutamic acid Phosphorylated

intermediate
NH3
P
ADP NH2 ADP Pi
Glu Glu
Phosphorylated Glutamine
intermediate
(b) Conversion reaction coupled with ATP hydrolysis

Figure 6.9-3
NH3 NH2
Glu ATP ADP P i
Glu

GATP = 7.3 kcal/mol
+ GATP = 7.3 kcal/mol
Net G = 3.9 kcal/mol (c) Free-energy change for coupled reaction

 Transport and mechanical work in the cell are
powered by ATP hydrolysis
 ATP hydrolysis leads to a change in a protein’s
shape and often its ability to bind to another
molecule

Figure 6.10
Transport protein Solute
ATP ADP Pi
P Pi
Solute transported
(a) Transport work: ATP phosphorylates transport proteins.
Vesicle Cytoskeletal track
ATP ADP Pi
ATP
Motor protein Protein and vesicle moved

(b) Mechanical work: ATP binds noncovalently to motor proteins
and then is hydrolyzed.
The Regeneration of ATP
 ATP is a renewable resource that is regenerated by

addition of a phosphate group to adenosine
diphosphate (ADP)
 The energy to phosphorylate ADP comes from
catabolic reactions in the cell
 The ATP cycle is a revolving door through which
energy passes during its transfer from catabolic to
anabolic pathways

Figure 6.11
ATP H 2O
Energy from Energy for cellular

catabolism (exergonic, work (endergonic,
energy-releasing ADP Pi energy-consuming
processes) processes)

Concept 6.4: Enzymes speed up metabolic reactions
by lowering energy barriers
 A catalyst is a chemical agent that speeds up a
reaction without being consumed by the reaction
 An enzyme is a catalytic protein
 Hydrolysis of sucrose by the enzyme sucrase is an
example of an enzyme-catalyzed reaction

Figure 6.UN02
Sucrase
+ H2O +
O OH HO
Sucrose Glucose Fructose
(C12H22O11) (C6H12O6) (C6H12O6)

The Activation Energy Barrier
 Every chemical reaction between molecules

involves bond breaking and bond forming
 The initial energy needed to start a chemical
reaction is called the free energy of activation, or
activation energy (EA)
 Activation energy often occurs in the form of heat
that reactant molecules absorb from the
surroundings

Figure 6.12
A B
C D
Transition state
A B EA
Free energy
C D
Reactants
A B
G < 0
C D
Products

How Enzymes Speed Up Reactions
 Instead of relying on heat, organisms carry out

catalysis to speed up reactions
 A catalyst (for example, an enzyme) can speed up a
reaction by lowering the EA barrier without itself
being consumed
 Enzymes do not affect the change in free energy
(∆G); instead, they hasten reactions that would
occur eventually

Animation: How Enzymes Work

Figure 6.13
Course of
reaction EA
without without
enzyme enzyme EA with
enzyme
is lower
Reactants
Free energy
Course of G is unaffected
reaction by enzyme
with enzyme
Products

Substrate Specificity of Enzymes
 Enzymes are very specific for the reactions they

catalyze
 The reactant that an enzyme acts on is called the
enzyme’s substrate
 The enzyme binds to its substrate, forming an
enzyme-substrate complex
 The active site is the region on the enzyme where
the substrate binds

 Enzyme specificity results from the complementary
fit between the shape of the enzyme’s active site
and the shape of the substrate
 Enzymes change shape due to chemical
interactions with the substrate
 This induced fit of the enzyme to the substrate
brings chemical groups of the active site together

Video: Enzyme Induced Fit

Figure 6.14
Substrate
Active site
Enzyme Enzyme-substrate
complex

Catalysis in the Enzyme’s Active Site
 In an enzymatic reaction, the substrate binds to the

active site of the enzyme
 The active site can lower an EA barrier by
 Orienting substrates correctly
 Straining substrate bonds
 Providing a favorable microenvironment
 Covalently bonding to the substrate

Figure 6.15-s1
Substrates enter Substrates are
active site. held in active site by
weak interactions.
Substrates
Enzyme-substrate
complex

Figure 6.15-s2
weak interactions.
Substrates
Enzyme-substrate
complex
Substrates are
converted to
products.
Figure 6.15-s3
weak interactions.
Substrates
Enzyme-substrate
complex
Products are
released. Substrates are
converted to
Products products.
Figure 6.15-s4
weak interactions.
Substrates
Enzyme-substrate
complex
Active site
is available
for new
substrates.
Enzyme
Products are
released. Substrates are
converted to
Products products.
 The rate of enzyme catalysis can usually be sped
up by increasing the substrate concentration in a
solution
 When all enzyme molecules in a solution are
bonded with substrate, the enzyme is saturated
 At enzyme saturation, reaction speed can only be
increased by adding more enzyme

Effects of Local Conditions on Enzyme Activity
 An enzyme’s activity can be affected by

 General environmental factors, such as temperature
and pH
 Chemicals that specifically influence the enzyme

Effects of Temperature and pH
 Each enzyme has an optimal temperature and pH at

which its reaction rate is the greatest

Figure 6.16
Optimal temperature for Optimal temperature for

typical human enzyme (37C) enzyme of thermophilic
(heat-loving)
bacteria (75C)
Rate of reaction
0 20
60 80 40 100 120
Temperature (C)
(a) Optimal temperature for two enzymes
Optimal pH for pepsin Optimal pH for trypsin

(stomach (intestinal
enzyme) enzyme)
Rate of reaction
0 1 5 2 3 4 6 7 8 9 10
pH
(b) Optimal pH for two enzymes
Figure 6.16-1
Optimal temperature for Optimal temperature for

typical human enzyme (37C) enzyme of thermophilic
(heat-loving)
Rate of reaction
bacteria (75C)
0 20
60 40
80 100 120
Temperature (C)
(a) Optimal temperature for two enzymes

Figure 6.16-2
Optimal pH for pepsin Optimal pH for trypsin

(stomach (intestinal
enzyme) enzyme)
Rate of reaction
0 1 5 2 3 4 6 7 8 9 10
pH
(b) Optimal pH for two enzymes

Figure 6.16-3

Cofactors
 Cofactors are nonprotein enzyme helpers

 Cofactors may be inorganic (such as a metal in
ionic form) or organic
 An organic cofactor is called a coenzyme
 Most vitamins act as coenzymes or as the raw
materials from which coenzymes are made

Enzyme Inhibitors
 Competitive inhibitors bind to the active site of an

enzyme, competing with the substrate
 Noncompetitive inhibitors bind to another part of
an enzyme, causing the enzyme to change shape
and making the active site less effective
 Examples of inhibitors include toxins, poisons,
pesticides, and antibiotics

Figure 6.17
(a) Normal binding (b) Competitive inhibition (c) Noncompetitive

inhibition
Substrate
Active site
Competitive
inhibitor
Enzyme
Noncompetitive
inhibitor

The Evolution of Enzymes
 Most enzymes are proteins encoded by genes

 Changes (mutations) in genes lead to changes in
amino acid composition of an enzyme
 Altered amino acids in enzymes may alter their
activity or substrate specificity
 Under new environmental conditions a novel form of
an enzyme might be favored

Concept 6.5: Regulation of enzyme activity helps
control metabolism
 Chemical chaos would result if a cell’s metabolic
pathways were not tightly regulated
 A cell does this by switching on or off the genes that
encode specific enzymes or by regulating the
activity of enzymes

Allosteric Regulation of Enzymes
 Allosteric regulation may either inhibit or stimulate

an enzyme’s activity
 Allosteric regulation occurs when a regulatory
molecule binds to a protein at one site and affects
the protein’s function at another site

Allosteric Activation and Inhibition
 Most allosterically regulated enzymes are made

from polypeptide subunits
 Each enzyme has active and inactive forms
 The binding of an activator stabilizes the active form
of the enzyme
 The binding of an inhibitor stabilizes the inactive
form of the enzyme

Figure 6.18
(a) Allosteric activators and inhibitors (b) Cooperativity: another type of allosteric
activation
Allosteric enzyme Active site Substrate
with four subunits (one of four)
Regulatory
site (one Activator Inactive form Stabilized active form
of four) Active form Stabilized active form
Oscillation
Non-
functional
active site
Inhibitor
Inactive form Stabilized inactive form

Figure 6.18-1
(a) Allosteric activators and inhibitors
Allosteric enzyme Active site
with four subunits (one of four)
Regulatory
site (one Activator
of four) Active form Stabilized
active form
Oscillation
Non-
functional
active site
Inhibitor
Inactive form Stabilized
inactive form
 Cooperativity is a form of allosteric regulation that
can amplify enzyme activity
 One substrate molecule primes an enzyme to act on
additional substrate molecules more readily
 Cooperativity is allosteric because binding by a
substrate to one active site affects catalysis in a
different active site

Figure 6.18-2
(b) Cooperativity: another type of allosteric

activation
Substrate
Inactive form Stabilized active form

Feedback Inhibition
 In feedback inhibition, the end product of a

metabolic pathway shuts down the pathway
 Feedback inhibition prevents a cell from wasting
chemical resources by synthesizing more product
than is needed

Figure 6.19
Active site available
Threonine
in active site
Enzyme 1
(threonine
Isoleucine deaminase)
used up by
cell
Intermediate A
Feedback
inhibition Enzyme 2
Intermediate B
Enzyme 3
Intermediate C
Isoleucine
binds to
allosteric Enzyme 4
site.
Intermediate D
Enzyme 5
End product
(isoleucine)
Organization of Enzymes Within the Cell
 Structures within the cell help bring order to

metabolic pathways
 Some enzymes act as structural components of
membranes
 In eukaryotic cells, some enzymes reside in specific
organelles; for example, enzymes for cellular
respiration are located in mitochondria

Figure 6.20
Mitochondrion
The matrix contains

enzymes in solution that
are involved in one stage
of cellular respiration.
Enzymes for another

stage of cellular
1 mm
respiration are
embedded in the
inner membrane.
Figure 6.20-1
Mitochondrion
The matrix contains

enzymes in solution that
are involved in one stage
of cellular respiration.
Enzymes for another

stage of cellular
1 mm
respiration are
embedded in the
inner membrane.
Figure 6.UN03a

Figure 6.UN03b

Figure 6.UN04
Course of
reaction EA
without without
enzyme EA with
enzyme
enzyme
is lower
Reactants
Free energy
G is unaffected
Course of
by enzyme
reaction
with enzyme
Products

Figure 6.UN05

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CAMPBELL BIOLOGY IN FOCUS

URRY • CAIN • WASSERMAN • MINORSKY • REECE

© 2016 Pearson Education, Inc. SECOND EDITION

 The living cell is a miniature chemical factory where

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

 A metabolic pathway begins with a specific

© 2016 Pearson Education, Inc.

Enzyme 1 Enzyme 2 Enzyme 3

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

 Energy is the capacity to cause change

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

Climbing up converts the kinetic A diver has less

 Thermodynamics is the study of energy

© 2016 Pearson Education, Inc.

 According to the first law of thermodynamics, the

© 2016 Pearson Education, Inc.

(a) First law of thermodynamics (b) Second law of thermodynamics

© 2016 Pearson Education, Inc.

(a) First law of thermodynamics

© 2016 Pearson Education, Inc.

 During every energy transfer or transformation,

© 2016 Pearson Education, Inc.

(b) Second law of thermodynamics

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

 Cells create ordered structures from less ordered

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

 A living system’s free energy is energy that can do

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

• More free energy (higher G)

• Less free energy (lower G)

© 2016 Pearson Education, Inc.

• More free energy (higher G)

• Less free energy (lower G)

(a) Gravitational (b) Diffusion (c) Chemical

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.

 The concept of free energy can be applied to the

© 2016 Pearson Education, Inc.

 An exergonic reaction proceeds with a net release

© 2016 Pearson Education, Inc.

(a) Exergonic reaction: energy released, spontaneous

Progress of the reaction

(b) Endergonic reaction: energy required,

Progress of the reaction

(a) Exergonic reaction: energy released, spontaneous

Progress of the reaction

© 2016 Pearson Education, Inc.

© 2016 Pearson Education, Inc.